-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_52

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for Augustus_model.g40626.t1
Valid prediction for GlimmerHMM_glimmerT_61068-T1
Valid prediction for GeneMark_model.106279_t
Valid prediction for snap_scaffold_52-snap.7-T1
Valid prediction for HiQ_model.g40623.t1
Valid prediction for snap_scaffold_52-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_61070-T1
Valid prediction for HiQ_model.g40624.t1
Valid prediction for snap_scaffold_52-snap.4-T1
Couldn't classify 10559, 10702
Sorry, prediction pasa_asmbl_46478.p1 fails validation.
(AGG)	 CC	10559-10702	GT	TGG
(GAC)	 AG	11181-11929	GT	AGG
(GTC)	 AG	12164-12317	GT	CGG
(GTG)	 AG	12655-12834	GT	TGG
(TGG)	 AG	13235-13480	GT	CTG
(CCT)	 AG	13863-14098	GT	AGG
(CAT)	 AG	14425-14518	GT	AGG
(GTC)	 AG	14641-14725	GT	TGG
(GTA)	 AG	14881-15017	AG	AGA
-recovered pasa_asmbl_46478.p1, terminal, 14881, 15017
-recovered pasa_asmbl_46478.p1, internal, 11181, 11929
-recovered pasa_asmbl_46478.p1, internal, 12164, 12317
-recovered pasa_asmbl_46478.p1, internal, 12655, 12834
-recovered pasa_asmbl_46478.p1, internal, 13235, 13480
-recovered pasa_asmbl_46478.p1, internal, 13863, 14098
-recovered pasa_asmbl_46478.p1, internal, 14425, 14518
-recovered pasa_asmbl_46478.p1, internal, 14641, 14725
Valid prediction for GeneMark_model.106278_t
Couldn't classify 6242, 6285
Couldn't classify 6561, 6625
Sorry, prediction CodingQuarry_transcript_52370-T1 fails validation.
(ATG)	 CA	5975-6083	GT	AGG
(ACT)	 AG	6242-6285	AT	GAA
(ATA)	 AC	6561-6625	GT	GTG
(TCA)	 AG	6930-7104	GG	AGG
-recovered CodingQuarry_transcript_52370-T1, initial, 5975, 6083
-recovered CodingQuarry_transcript_52370-T1, terminal, 6930, 7104
Valid prediction for snap_scaffold_52-snap.6-T1
Valid prediction for GeneMark_model.106276_t
Valid prediction for snap_scaffold_52-snap.2-T1
Couldn't classify 6242, 6285
Couldn't classify 6561, 6625
Sorry, prediction pasa_asmbl_46477.p1 fails validation.
(ATG)	 CA	5975-6083	GT	AGG
(ACT)	 AG	6242-6285	AT	GAA
(ATA)	 AC	6561-6625	GT	GTG
(TCA)	 AG	6930-7104	GG	AGG
-recovered pasa_asmbl_46477.p1, initial, 5975, 6083
-recovered pasa_asmbl_46477.p1, terminal, 6930, 7104
Valid prediction for GlimmerHMM_glimmerT_61067-T1
Couldn't classify 25582, 25609
Sorry, prediction GeneMark_model.106281_t fails validation.
(ATG)	 TG	24562-24716	GT	AGG
(GTC)	 AG	24862-25551	GT	AGG
(GGC)	 AG	25582-25609	GT	AGG
-recovered GeneMark_model.106281_t, initial, 24562, 24716
-recovered GeneMark_model.106281_t, internal, 24862, 25551
-recovered GeneMark_model.106281_t, internal, 25582, 25609
Valid prediction for snap_scaffold_52-snap.3-T1
Valid prediction for GeneMark_model.106277_t

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Couldn't classify 27479, 27644
Sorry, prediction HiQ_model.g40622.t1 fails validation.
(ATG)	 TA	22944-23029	GT	AGG
(GAG)	 AG	23353-23686	GT	TGG
(CTG)	 AG	23841-23996	GT	AGG
(GGT)	 AG	24078-24172	GT	AGG
(GCA)	 AG	25056-25161	GT	AGG
(GGC)	 AG	25239-25400	GT	AGG
(CTG)	 AG	25517-25602	GT	AAG
(GCT)	 AG	25685-25782	GT	CTG
(GTA)	 AG	25880-25985	GT	AGG
(GTC)	 AG	26072-26105	GT	AAG
(ATG)	 AG	26254-26390	GC	AGG
(TTA)	 AG	26497-26591	GT	AGG
(GAA)	 AG	27479-27644	GT	ATG
-recovered HiQ_model.g40622.t1, initial, 22944, 23029
-recovered HiQ_model.g40622.t1, initial, 26254, 26390
add_exon() Sorry, HiQ_model.g40622.t1 25517-25602-terminal-2 is invalid.
-recovered HiQ_model.g40622.t1, terminal, 25517, 25602
-recovered HiQ_model.g40622.t1, internal, 23353, 23686
-recovered HiQ_model.g40622.t1, internal, 23841, 23996
-recovered HiQ_model.g40622.t1, internal, 24078, 24172
-recovered HiQ_model.g40622.t1, internal, 25056, 25161
-recovered HiQ_model.g40622.t1, internal, 25239, 25400
-recovered HiQ_model.g40622.t1, internal, 25517, 25602
-recovered HiQ_model.g40622.t1, internal, 25685, 25782
-recovered HiQ_model.g40622.t1, internal, 25880, 25985
-recovered HiQ_model.g40622.t1, internal, 26072, 26105
-recovered HiQ_model.g40622.t1, internal, 26254, 26390
-recovered HiQ_model.g40622.t1, internal, 26497, 26591
-recovered HiQ_model.g40622.t1, internal, 27479, 27644
Valid prediction for GlimmerHMM_glimmerT_61069-T1
Valid prediction for CodingQuarry_transcript_52369-T1
Valid prediction for GlimmerHMM_glimmerT_61066-T1
Valid prediction for Augustus_model.g40625.t1
Valid prediction for GeneMark_model.106280_t
Valid prediction for snap_scaffold_52-snap.8-T1
Couldn't classify 27479, 27612
Sorry, prediction pasa_asmbl_46483.p1 fails validation.
(ATG)	 AC	22932-23029	GT	AGG
(GAG)	 AG	23353-23686	GT	TGG
(CTG)	 AG	23841-23996	GT	AGG
(GGT)	 AG	24078-24172	GT	AGG
(GCA)	 AG	25056-25161	GT	AGG
(GGC)	 AG	25239-25400	GT	AGG
(CTG)	 AG	25517-25602	GT	AAG
(GCT)	 AG	25685-25782	GT	CTG
(GTA)	 AG	25880-25985	GT	AGG
(GTC)	 AG	26072-26105	GT	AAG
(ATG)	 AG	26254-26390	GC	AGG
(TTA)	 AG	26497-26591	GT	AGG
(GAA)	 AG	27479-27612	GT	AGG
-recovered pasa_asmbl_46483.p1, initial, 22932, 23029
-recovered pasa_asmbl_46483.p1, initial, 26254, 26390
add_exon() Sorry, pasa_asmbl_46483.p1 25517-25602-terminal-2 is invalid.
-recovered pasa_asmbl_46483.p1, terminal, 25517, 25602
-recovered pasa_asmbl_46483.p1, internal, 23353, 23686
-recovered pasa_asmbl_46483.p1, internal, 23841, 23996
-recovered pasa_asmbl_46483.p1, internal, 24078, 24172
-recovered pasa_asmbl_46483.p1, internal, 25056, 25161
-recovered pasa_asmbl_46483.p1, internal, 25239, 25400
-recovered pasa_asmbl_46483.p1, internal, 25517, 25602
-recovered pasa_asmbl_46483.p1, internal, 25685, 25782
-recovered pasa_asmbl_46483.p1, internal, 25880, 25985
-recovered pasa_asmbl_46483.p1, internal, 26072, 26105
-recovered pasa_asmbl_46483.p1, internal, 26254, 26390
-recovered pasa_asmbl_46483.p1, internal, 26497, 26591
-recovered pasa_asmbl_46483.p1, internal, 27479, 27612
Valid prediction for GeneMark_model.106275_t
Valid prediction for snap_scaffold_52-snap.1-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)
-building DP trellis

-building trellis in range 1 - 27771
-exon list size: 123


building trellis

0.8    
1.6    
2.4    
3.2    
4.0    
4.8    
5.6    
6.4    
7.2    
8.0    
8.8    
9.6    
10.4    
11.2    
12.0    
12.8    
13.6    
14.4    
15.2    
16.0    
16.8    
17.6    
18.4    
19.2    
20.0    
20.8    
21.6    
22.4    
23.2    
24.0    
24.8    
25.6    
26.4    
27.2    
28.0    
28.8    
29.6    
30.4    
31.2    
32.0    
32.8    
33.6    
34.4    
35.2    
36.0    
36.8    
37.6    
38.4    
39.2    
40.0    
40.8    
41.6    
42.4    
43.2    
44.0    
44.8    
45.6    
46.4    
47.2    
48.0    
48.8    
49.6    
50.4    
51.2    
52.0    
52.8    
53.6    
54.4    
55.2    
56.0    
56.8    
57.6    
58.4    
59.2    
60.0    
60.8    
61.6    
62.4    
63.2    
64.0    
64.8    
65.6    
66.4    
67.2    
68.0    
68.8    
69.6    
70.4    
71.2    
72.0    
72.8    
73.6    
74.4    
75.2    
76.0    
76.8    
77.6    
78.4    
79.2    
80.0    
80.8    
81.6    
82.4    
83.2    
84.0    
84.8    
85.6    
86.4    
87.2    
88.0    
88.8    
89.6    
90.4    
91.2    
92.0    
92.8    
93.6    
94.4    
95.2    
96.0    
96.8    
97.6    
98.4    
99.2    
-found 7 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 5 predictions persist after filtering for low support